How to use multi_cox.r in R language
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Multi_cox.r multivariate cox analysis
How to use it:
Multiple gene expressions were designated for multivariate cox regression analysis, and the prognostic models were constructed and evaluated.
$Rscript $scriptdir/multi_cox.r-husage: / share/nas1/huangls/test/TCGA_immu/scripts/multi_cox.r [- h]-I data-t time-e event-v variate [variate...] [- P predict.time [predict.time...]] [- c cut.score] [- s seed] [- o outdir] [- p prefix] multi variate cox regression analysis using gene expressionoptional arguments:-h -- help show this help message and exit-I data,-- data data input data file path [required]-t time,-- time time set suvival time column name [required]-e event,-- event event set event column name must 0 or 1 code format [required]-v variate [variate...],-- variate variate [variate...] Variate for cox analysis [required]-P predict.time [predict.time...],-- predict.time predict.time [predict.time...] Time point to draw the ROC curve [default 1095 1825]-c cut.score,-- cut.score cut.score set cut score value to divide high and low risk groups [default median]-s seed,-- seed seed set random seed [default 2021]-o outdir,-- outdir outdir output file directory [default cwd]-p prefix -- prefix prefix out file name prefix [default cox] example: Rscript $scriptdir/multi_cox.r-I imm.unicox.metadata-exp.tsv-e EVENT-t TIME\-v PDGFRL CXCR4 PAK3 CSF1R PDCD1-P 1095 1825\-o multicox-p multicox parameter description:
-I input survival data and gene expression files
BarcodeTIMEEVENTFGRCD38ITGALCX3CL1CEACAM21MATKCD79BMMP25TCGA-B7-A5TK-01A-12R-A36D-31288016.3440886.8677240.26903603.01321.8685362.283423.45319813.72829TCGA-BR-7959-01A-11R-2343-131010011.9673915.794517.35856626.913532.5719170.8641161.8799573.451148TCGA-IN-8462-01A-11R-2343-1357205.3508463.1113423.76912520.222380.6108390.5197762.8221921.106563TCGA-CG-4443-01A-01R-1157-1391201.538020.8629552.3735119.040971.0921270.7603481.9265920.878735TCGAMube A93JMuir 01A- 11R-A39E-311124015.2401613.304738.0859114.152953.4835593.1929513.65174210.43186TCGA-HU-A4H3-01A-21R-A251-3188206.2617612.6751737.0258864.0502710.5841591.0393361.9792142.312993TCGA-RD-A8MV-01A-11R-A36D-313720027.0741520.1588534.9130934.718214.1131122.61555716.5194617.72674TCGA-VQ-A91X-01A-12R-A414-3128911.0623410.7520182.3805134.4158150.5181420.2121971.2392030.582114
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